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HMMGraph.C
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HMMGraph.C
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/**************************************************************
HMMGraph.C
bmajoros@tigr.org
Copyright (c) 2003, The Institute for Genomic Research (TIGR),
Rockville, Maryland, U.S.A. All rights reserved.
***************************************************************/
#include "HMMGraph.H"
#include <iostream>
#include <math.h>
using namespace std;
HMMGraph::HMMGraph(HiddenMarkovModel &hmm)
: hmm(hmm), predecessors(hmm.countStates()),
emissions(hmm.getAlphabet().getNumElements())
{
// ctor
init();
}
void HMMGraph::init()
{
int numStates=hmm.countStates();
for(int i=0 ; i<numStates ; ++i)
for(int j=0 ; j<numStates ; ++j)
{
double p=hmm.getTransitionProb(i,j);
if(p>0)
predecessors[j].push_back(StateDoublePair(i,log(p),p));
}
Alphabet &alphabet=hmm.getAlphabet();
int numSymbols=alphabet.getNumElements();
for(int state=0 ; state<numStates ; ++state)
for(int symbol=0 ; symbol<numSymbols ; ++symbol)
{
double p=hmm.getEmissionProb(state,symbol);
if(p>0)
emissions[symbol].push_back(StateDoublePair(state,log(p),p));
}
}
TigrVector<StateDoublePair> &HMMGraph::statesEmitting(Symbol s)
{
return emissions[s];
}
TigrVector<StateDoublePair> &HMMGraph::statesPreceding(int state)
{
return predecessors[state];
}
HiddenMarkovModel &HMMGraph::getHMM()
{
return hmm;
}